Showing 18 of total 18 results (show query)
r-forge
Matrix:Sparse and Dense Matrix Classes and Methods
A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.
Maintained by Martin Maechler. Last updated 20 days ago.
1 stars 17.23 score 33k scripts 12k dependents
bioc
BiocGenerics:S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructurebioconductor-packagecore-package
12 stars 14.22 score 612 scripts 2.2k dependents
tomoakin
RPostgreSQL:R Interface to the 'PostgreSQL' Database System
Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems. In order to build and install this package from source, 'PostgreSQL' itself must be present your system to provide 'PostgreSQL' functionality via its libraries and header files. These files are provided as 'postgresql-devel' package under some Linux distributions. On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Maintained by Tomoaki Nishiyama. Last updated 2 days ago.
66 stars 12.11 score 4.5k scripts 19 dependentsr-forge
copula:Multivariate Dependence with Copulas
Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.
Maintained by Martin Maechler. Last updated 25 days ago.
11.83 score 1.2k scripts 86 dependentsr-forge
Rmpfr:Interface R to MPFR - Multiple Precision Floating-Point Reliable
Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Maintained by Martin Maechler. Last updated 5 months ago.
11.30 score 316 scripts 141 dependentsbioc
BASiCS:Bayesian Analysis of Single-Cell Sequencing data
Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.
Maintained by Catalina Vallejos. Last updated 5 months ago.
immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecelldifferentialexpressionbayesiancellbiologybioconductor-packagegene-expressionrcpprcpparmadilloscrna-seqsingle-cellopenblascppopenmp
83 stars 10.14 score 368 scripts 1 dependents
polmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
49 stars 7.96 score 311 scriptsbioc
motifStack:Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
Maintained by Jianhong Ou. Last updated 3 months ago.
sequencematchingvisualizationsequencingmicroarrayalignmentchipchipchipseqmotifannotationdataimport
7.93 score 188 scripts 6 dependents
drjphughesjr
hash:Full Featured Implementation of Hash Tables/Associative Arrays/Dictionaries
Implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.
Maintained by John Hughes. Last updated 2 years ago.
1 stars 7.54 score 4.0k scripts 50 dependents
jamovi
jmvcore:Dependencies for the 'jamovi' Framework
A framework for creating rich interactive analyses for the jamovi platform (see <https://www.jamovi.org> for more information).
Maintained by Jonathon Love. Last updated 7 months ago.
4 stars 6.51 score 20 scripts 8 dependents
mjskay
ggblend:Blending and Compositing Algebra for 'ggplot2'
Algebra of operations for blending, copying, adjusting, and compositing layers in 'ggplot2'. Supports copying and adjusting the aesthetics or parameters of an existing layer, partitioning a layer into multiple pieces for re-composition, applying affine transformations to layers, and combining layers (or partitions of layers) using blend modes (including commutative blend modes, like multiply and darken). Blend mode support is particularly useful for creating plots with overlapping groups where the layer drawing order does not change the output; see Kindlmann and Scheidegger (2014) <doi:10.1109/TVCG.2014.2346325>.
Maintained by Matthew Kay. Last updated 2 years ago.
186 stars 6.30 score 71 scripts 1 dependentsbioc
CellBarcode:Cellular DNA Barcode Analysis toolkit
The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.
Maintained by Wenjie Sun. Last updated 8 days ago.
preprocessingqualitycontrolsequencingcrisprampliconamplicon-sequencingcellular-barcodecpp
1 stars 5.86 score 40 scripts
eddelbuettel
RcppBDT:'Rcpp' Bindings for the Boost Date_Time Library
Access to Boost Date_Time functionality for dates, durations (both for days and date time objects), time zones, and posix time ('ptime') is provided by using 'Rcpp modules'. The posix time implementation can support high-resolution of up to nano-second precision by using 96 bits (instead of 64 with R) to present a 'ptime' object (but this needs recompilation with a #define set).
Maintained by Dirk Eddelbuettel. Last updated 19 days ago.
17 stars 5.01 score 6 scripts 1 dependents
spkaluzny
splusTimeDate:Times and Dates from 'S-PLUS'
A collection of classes and methods for working with times and dates. The code was originally available in 'S-PLUS'.
Maintained by Stephen Kaluzny. Last updated 2 months ago.
4.94 score 58 scripts 2 dependentsspkaluzny
splusTimeSeries:Time Series from 'S-PLUS'
A collection of classes and methods for working with indexed rectangular data. The index values can be calendar (timeSeries class) or numeric (signalSeries class). Methods are included for aggregation, alignment, merging, and summaries. The code was originally available in 'S-PLUS'.
Maintained by Stephen Kaluzny. Last updated 6 months ago.
3.95 score 20 scripts 1 dependents
cran
arulesSequences:Mining Frequent Sequences
Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.
Maintained by Christian Buchta. Last updated 7 months ago.
12 stars 2.63 score
davidruvolo51
rdConvert:Convert Rd files to Markdown files loaded with YAML
As R6 class for converting Rd files to markdown with YAML headers. This may be useful if you wish to use package documentation in static site generators outside of the R ecosystem (e.g., React, Vue, Svelte, Gatsby, etc.). By default, Rd files are rendered into their own directory with an independent `index.md` file. The Rd name is parsed and set as the child directory name.
Maintained by David Ruvolo. Last updated 4 years ago.
gatsby-templatepackage-developmentrmarkdownrmarkdown-websitesworkflow
3 stars 2.18 score